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Photoinduced deoxyribose C2′ oxidation in DNA. Alkali-dependent cleavage of erythrose-containing sites via a retroaldol reaction
Photoreactions of various 5-iodouracil- (1U)-containing oligonucleotides have been investigated. It was found that d(GCA1UGC)2 undergoes a competitive Cl′ and C2′ oxidation at the 5′ side of the 1U residue to give deoxyribonolactone-containing hexamer 1 and erythrose-containing hexamer 2, respectively. Upon heating under alkaline conditions, erythrose-containing hexamer 2 was shown to undergo a remarkably facile retroaldol reaction to give two fragments, both having phosphoroglycoaldehyde termini in high yields. On the basis of the chemical reactivity of 2, a new specific method for detection of the erythrose-containing sites resulting from deoxyribose C2′ oxidation in DNA was devised. Erythrose-containing sites were prepared by photoirradiation of duplex 1U-containing 13 mer 5′-d(CG1UGT'UTA1UAC 1UG)-3′/5′-d(CAGTATAAACACG)-3′. After photoirradiation, the reaction mixture was treated with hot alkali and NaBH4 and then subjected to enzymatic digestion. HPLC analysis of the digested mixture revealed the formation of modified mononucleotides 25-28, allowing the quantification of the erythrose-containing sites being produced at the 5′ side of all four 1U residues of the 13 mer. These results indicate that this method can be used for the detection and quantification of erythrose-containing sites resulting from deoxyribose C2′ oxidation in DNA.
Sugiyama, Hiroshi,Tsutsumi, Yasushi,Fujimoto, Kenzo,Saito, Isao
p. 4443 - 4448
(1993)
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Gatlin,Davis
p. 4464,4465,4469
(1962)
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The Peculiar Case of the Hyper-thermostable Pyrimidine Nucleoside Phosphorylase from Thermus thermophilus**
The poor solubility of many nucleosides and nucleobases in aqueous solution demands harsh reaction conditions (base, heat, cosolvent) in nucleoside phosphorylase-catalyzed processes to facilitate substrate loading beyond the low millimolar range. This, in turn, requires enzymes that can withstand these conditions. Herein, we report that the pyrimidine nucleoside phosphorylase from Thermus thermophilus is active over an exceptionally broad pH (4–10), temperature (up to 100 °C) and cosolvent space (up to 80 % (v/v) nonaqueous medium), and displays tremendous stability under harsh reaction conditions with predicted total turnover numbers of more than 106 for various pyrimidine nucleosides. However, its use as a biocatalyst for preparative applications is critically limited due to its inhibition by nucleobases at low concentrations, which is unprecedented among nonspecific pyrimidine nucleoside phosphorylases.
Kaspar, Felix,Neubauer, Peter,Kurreck, Anke
p. 1385 - 1390
(2021/01/29)

Thermodynamic Reaction Control of Nucleoside Phosphorolysis
Nucleoside analogs represent a class of important drugs for cancer and antiviral treatments. Nucleoside phosphorylases (NPases) catalyze the phosphorolysis of nucleosides and are widely employed for the synthesis of pentose-1-phosphates and nucleoside analogs, which are difficult to access via conventional synthetic methods. However, for the vast majority of nucleosides, it has been observed that either no or incomplete conversion of the starting materials is achieved in NPase-catalyzed reactions. For some substrates, it has been shown that these reactions are reversible equilibrium reactions that adhere to the law of mass action. In this contribution, we broadly demonstrate that nucleoside phosphorolysis is a thermodynamically controlled endothermic reaction that proceeds to a reaction equilibrium dictated by the substrate-specific equilibrium constant of phosphorolysis, irrespective of the type or amount of NPase used, as shown by several examples. Furthermore, we explored the temperature-dependency of nucleoside phosphorolysis equilibrium states and provide the apparent transformed reaction enthalpy and apparent transformed reaction entropy for 24 nucleosides, confirming that these conversions are thermodynamically controlled endothermic reactions. This data allows calculation of the Gibbs free energy and, consequently, the equilibrium constant of phosphorolysis at any given reaction temperature. Overall, our investigations revealed that pyrimidine nucleosides are generally more susceptible to phosphorolysis than purine nucleosides. The data disclosed in this work allow the accurate prediction of phosphorolysis or transglycosylation yields for a range of pyrimidine and purine nucleosides and thus serve to empower further research in the field of nucleoside biocatalysis. (Figure presented.).
Kaspar, Felix,Giessmann, Robert T.,Neubauer, Peter,Wagner, Anke,Gimpel, Matthias
supporting information
p. 867 - 876
(2020/01/24)

Efficient biocatalytic synthesis of dihalogenated purine nucleoside analogues applying thermodynamic calculations
The enzymatic synthesis of nucleoside analogues has been shown to be a sustainable and efficient alternative to chemical synthesis routes. In this study, dihalogenated nucleoside analogues were produced by thermostable nucleoside phosphorylases in transglycosylation reactions using uridine or thymidine as sugar donors. Prior to the enzymatic process, ideal maximum product yields were calculated after the determination of equilibrium constants through monitoring the equilibrium conversion in analytical-scale reactions. Equilibrium constants for dihalogenated nucleosides were comparable to known purine nucleosides, ranging between 0.071 and 0.081. To achieve 90% product yield in the enzymatic process, an approximately five-fold excess of sugar donor was needed. Nucleoside analogues were purified by semi-preparative HPLC, and yields of purified product were approximately 50% for all target compounds. To evaluate the impact of halogen atoms in positions 2 and 6 on the antiproliferative activity in leukemic cell lines, the cytotoxic potential of dihalogenated nucleoside analogues was studied in the leukemic cell line HL-60. Interestingly, the inhibition of HL-60 cells with dihalogenated nucleoside analogues was substantially lower than with monohalogenated cladribine, which is known to show high antiproliferative activity. Taken together, we demonstrate that thermodynamic calculations and small-scale experiments can be used to produce nucleoside analogues with high yields and purity on larger scales. The procedure can be used for the generation of new libraries of nucleoside analogues for screening experiments or to replace the chemical synthesis routes of marketed nucleoside drugs by enzymatic processes.
Giessmann, Robert T.,Kaspar, Felix,Klare, Hendrik F. T.,Kurreck, Jens,Neubauer, Peter,Paulick, Katharina,R?hrs, Viola,Wagner, Anke,Westarp, Sarah,Yehia, Heba
(2020/02/28)

Sources of 2,5-diaminoimidazolone lesions in DNA damage initiated by hydroxyl radical attack
The present study reports radiation-chemical yields of 2.5-diaminoimidazolone (Iz) derivatives in X-irradiated phosphate-buffered solutions of guanosine and double-stranded DNA. Various gassing conditions (air, N20/O2 (4:1), N2O, vacuum) were employed to elucidate the contribution of several alternative pathways leading to Iz in reactions initiated by hydroxyl radical attack on guanine. In all systems, Iz was identified as the second by abundance guanine degradation product after 8-oxoguanine, formed in 1:5 (guanosine) and 1:3.3 (DNA) ratio to the latter in air-saturated solutions. Experimental data strongly suggest that the addition of molecular oxygen to the neutral guanine radical G(-H)? plays a major in Iz production in oxygenated solutions of double-stranded DNA while in other systems it may compete with recombination of G(-H)? with superoxide and/or alkyl peroxyl radicals. The production of Iz through hydroxyl radical attack on 8-oxoguanine was also shown to take place although the chemical yield of Iz (ca 6%) in this process is too low to compete with the other pathways. The linearity of Iz accumulation with dose also indicates a negligible contribution of this channel to its yield in all systems.
Thomas, Caroline Suzanne,Pollard, Hannah Catherine,Razskazovskiy, Yuriy,Roginskaya, Marina
p. 517 - 524
(2020/09/07)

Anion exchange resins in phosphate form as versatile carriers for the reactions catalyzed by nucleoside phosphorylases
In the present work, we suggested anion exchange resins in the phosphate form as a source of phosphate, one of the substrates of the phosphorolysis of uridine, thymidine, and 1-(β-D-arabinofuranosyl)uracil (Ara-U) catalyzed by recombinant E. coli uridine (UP) and thymidine (TP) phosphorylases. α-D-Pentofuranose-1-phosphates (PF-1Pis) obtained by phosphorolysis were used in the enzymatic synthesis of nucleosides. It was found that phosphorolysis of uridine, thymidine, and Ara-U in the presence of Dowex 1X8 (phosphate; Dowex-nPi) proceeded smoothly in the presence of magnesium cations in water at 20-50 °C for 54-96 h giving rise to quantitative formation of the corresponding pyrimidine bases and PF-1Pis. The resulting PF-1Pis can be used in three routes: (1) preparation of barium salts of PF-1Pis, (2) synthesis of nucleosides by reacting the crude PF-1Pi with an heterocyclic base, and (3) synthesis of nucleosides by reacting the ionically bound PF-1Pi to the resin with an heterocyclic base. These three approaches were tested in the synthesis of nelarabine, kinetin riboside, and cladribine with good to excellent yields (52-93%).
Artsemyeva, Julia N.,Buravskaya, Tatiana N.,Esipov, Roman S.,Konstantinova, Irina D.,Litvinko, Natalia M.,Mikhailopulo, Igor A.,Miroshnikov, Anatoly I.,Remeeva, Ekaterina A.
p. 2607 - 2622
(2020/11/26)

Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: A backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography
Oligodeoxynucleotides incorporating internucleotide phosphoroselenolate linkages have been prepared under solid-phase synthesis conditions using dimer phosphoramidites. These dimers were constructed following the high yielding Michaelis-Arbuzov (M-A) reaction of nucleoside H-phosphonate derivatives with 5′-deoxythymidine-5′-selenocyanate and subsequent phosphitylation. Efficient coupling of the dimer phosphoramidites to solid-supported substrates was observed under both manual and automated conditions and required only minor modifications to the standard DNA synthesis cycle. In a further demonstration of the utility of M-A chemistry, the support-bound selenonucleoside was reacted with an H-phosphonate and then chain extended using phosphoramidite chemistry. Following initial unmasking of methyl-protected phosphoroselenolate diesters, pure oligodeoxynucleotides were isolated using standard deprotection and purification procedures and subsequently characterised by mass spectrometry and circular dichroism. The CD spectra of both modified and native duplexes derived from self-complementary sequences with A-form, B-form or mixed conformational preferences were essentially superimposable. These sequences were also used to study the effect of the modification upon duplex stability which showed context-dependent destabilisation (-0.4 to-3.1 °C per phosphoroselenolate) when introduced at the 5′-Termini of A-form or mixed duplexes or at juxtaposed central loci within a B-form duplex (-1.0 °C per modification). As found with other nucleic acids incorporating selenium, expeditious crystallisation of a modified decanucleotide A-form duplex was observed and the structure solved to a resolution of 1.45 ?. The DNA structure adjacent to the modification was not significantly perturbed. The phosphoroselenolate linkage was found to impart resistance to nuclease activity.
Conlon, Patrick F.,Eguaogie, Olga,Wilson, Jordan J.,Sweet, Jamie S. T.,Steinhoegl, Julian,Englert, Klaudia,Hancox, Oliver G. A.,Law, Christopher J.,Allman, Sarah A.,Tucker, James H. R.,Hall, James P.,Vyle, Joseph S.
p. 10948 - 10957
(2019/12/23)

Biomimetic Oxidative Deamination Catalysis via ortho-Naphthoquinone-Catalyzed Aerobic Oxidation Strategy
An ortho-naphthoquinone-catalyzed oxidative deamination reaction has been developed where the molecular oxygen and water serve as the sole oxidant and nucleophile. The current aerobic deamination reaction proceeds via the ketimine formation between ortho-naphthoquinones and amines followed by the prototropic rearrangement and hydrolysis by water, representing a biomimetic oxidative deamination of amine species in the human body by the liver and kidneys. The compatibility of ortho-naphthoquinone organocatalysts with molecular oxygen and water opens up a new biomimetic catalyst system that can function as versatile deaminases for a variety of amine-containing molecules such as amino acids and DNA nuclear bases.
Golime, Gangadhararao,Bogonda, Ganganna,Kim, Hun Young,Oh, Kyungsoo
p. 4986 - 4990
(2018/05/14)

Substrate specificity of E. coli uridine phosphorylase. Further evidences of high-syn conformation of the substrate in uridine phosphorolysis
Twenty five uridine analogues have been tested and compared with uridine with respect to their potency to bind to E. coli uridine phosphorylase. The kinetic constants of the phosphorolysis reaction of uridine derivatives modified at 2′-, 3′- and 5′-positions of the sugar moiety and 2-, 4-, 5- and 6-positions of the heterocyclic base were determined. The absence of the 2′- or 5′-hydroxyl group is not crucial for the successful binding and phosphorolysis. On the other hand, the absence of both the 2′- and 5′-hydroxyl groups leads to the loss of substrate binding to the enzyme. The same effect was observed when the 3′-hydroxyl group is absent, thus underlining the key role of this group. Our data shed some light on the mechanism of ribo- and 2′-deoxyribonucleoside discrimination by E. coli uridine phosphorylase and E. coli thymidine phosphorylase. A comparison of the kinetic results obtained in the present study with the available X-ray structures and analysis of hydrogen bonding in the enzyme-substrate complex demonstrates that uridine adopts an unusual high-syn conformation in the active site of uridine phosphorylase.
Alexeev,Sivets,Safonova,Mikhailov
p. 107 - 121
(2017/02/05)

Methyl ketone derivative, and preparation method and applications thereof
The invention discloses a methyl ketone derivative, and a preparation method and applications thereof. The preparation method comprises following steps: a ketone derivative and an organic peroxide are dissolved in a solvent, and reaction is carried out at 80 to 130 DEG C so as to obtain methyl pyrimidone and a methyl pyrimidone derivative. According to the preparation method, the ketone derivative is taken as a starting material; the raw materials are easily and widely available; products of different kinds can be obtained via the preparation method, and can be used directly or used in other further reaction. No metal is involved, so that the preparation method is suitable to be applied in pharmaceutical preparation technology. The preparation method is short in route, mild in reaction conditions, simple in reaction operation and postprocessing process, and high in yield, and is suitable for large-scale production.
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(2017/08/28)

Biotransformation of halogenated nucleosides by immobilized Lactobacillus animalis 2′-N-deoxyribosyltransferase
An immobilized biocatalyst with 2′-N-deoxyribosyltransferase (NDT) activity, Lactobacillus animalis NDT (LaNDT), was developed from cell free extracts. LaNDT was purified, characterized and then immobilized by ionic interaction. Different process parameters were optimized, resulting in an active derivative (2.6 U/g) able to obtain 1.75 mg/g of 5-fluorouracil-2′-deoxyriboside, an antimetabolite known as floxuridine, used in gastrointestinal cancer treatment. Furthermore, immobilized LaNDT was satisfactorily used to obtain at short reaction times other halogenated pyrimidine and purine 2′-deoxynucleosides such as 6-chloropurine-2′-deoxyriboside (4.9 U/g), 6-bromopurine-2′-deoxyriboside (4.3 U/g), 6-chloro-2-fluoropurine-2′-deoxyriboside (5.4 U/g), 5-bromo-2′-deoxyuridine (2.8 U/g) and 5-chloro-2′-deoxyuridine (1.8 U/g) compounds of pharmaceutical interest in antiviral or antitumor treatments. Besides, increasing the biocatalyst amount 8 times per volume unit allowed obtaining a 5-fold improvement in floxuridine biotransformation. The developed biocatalyst proved to be effective for the biosynthesis of a wide spectrum of nucleoside analogues by employing an economical, simple and environmentally friendly methodology.
Britos, Claudia N.,Lapponi, María José,Cappa, Valeria A.,Rivero, Cintia W.,Trelles, Jorge A.
p. 91 - 96
(2016/05/10)

Thymidylate synthase inspired biomodel reagent for the conversion of uracil to thymine
Inspired by TSase catalysis for dUMP conversion to dTMP, a biomodel reagent is developed. The presence of NH2, Gly-(S)-Cys and (S)-oxiran methyl, at C5, C4 and N-10 of acridine, respectively, in addition to the pH of the reaction mixture, allows for good complementary inter- and intra-molecular interactions and chiral discrimination for the reagent to achieve conversion of uracil to thymine.
Singh, Palwinder,Kumar, Arun,Kaur, Sukhmeet,Singh, Amrinder
supporting information
p. 9961 - 9964
(2015/06/22)

Mass spectrometry and theoretical studies on N-C bond cleavages in the N-sulfonylamidino thymine derivatives
Abstract The reactivity of new biologically active thymine derivatives substituted with 2-(arylsulfonamidino)ethyl group at N1 and N3 position was investigated in the gas phase using CID experiments (ESI-MS/MS) and by density functional theory (DFT) calculations. Both derivatives show similar chemistry in the negative mode with a retro-Michael addition (Path A-) being the most abundant reaction channel, which correlate well with the fluoride induced retro-Michael addition observed in solution. The difference in the fragmentation of N-3 substituted thymine 5 and N-1 substituted thymine 1 in the positive mode relates to the preferred cleavage of the sulfonyl group (m/z 155, Path B) in N-3 isomer and the formation of the acryl sulfonamidine 3 (m/z 309) via Path A in N-1 isomer. Mechanistic studies of the cleavage reaction conducted by DFT calculations give the trend of the calculated activation energies that agree well with the experimental observations. A mechanism of the retro-Michael reaction was interpreted as a McLafferty type of fragmentation, which includes Hβ proton shift to one of the neighboring oxygen atoms in a 1,5-fashion inducing N1(N3)-Cα bond scission. This mechanism was found to be kinetically favorable over other tested mechanisms. Significant difference in the observed fragmentation pattern of N-1 and N-3 isomers proves the ESI-MS/MS technique as an excellent method for tracking the fate of similar sulfonamidine drugs. Also, the observed N-1 and/or N-3 thymine alkylation with in situ formed reactive acryl sulfonamidine 3 as a Michael acceptor may open interesting possibilities for the preparation of other N-3 substituted pyrimidines.
Kobeti?, Renata,Kazazi?, Snje?ana,Kova?evi?, Borislav,Glasovac, Zoran,Krstulovi?, Luka,Baji?, Miroslav,?ini?, Biserka
p. 833 - 842
(2015/05/20)

Synthesis and stability of nucleoside 3a?2,5a?2-cyclic phosphate triesters masked with enzymatically and thermally labile phosphate protecting groups
Appropriately protected structurally modified nucleoside 3a?2,5a?2-cyclic monophosphates are known to show antiviral activity. For this reason, a straightforward synthesis of nucleoside 3a?2,5a?2-cyclic phosphates protected with three different enzymatically removable groups, viz. 3-acetyloxy-2,2-bis-(ethoxycarbonyl)propyl (in 1 and 4), 4-acetylthio-2,2-di-methyl-3-oxobutyl (in 2), and 4-(tert-butyldisulfanyl)-2,2-di-methyl-3-oxobutyl (in 3) groups, is described. Removal of these protecting groups at pH 7.5 and 37?°C was monitored by reverse-phase HPLC.
Sontakke, Vyankat A.,Shinde, Vaishali S.,L??nnberg, Harri,Ora, Mikko
p. 389 - 394
(2015/03/05)

Sonochemical transformation of thymidine: A mass spectrometric study
Abstract Ultrasound is extensively used in medical field for a number of applications including targeted killing of cancer cells. DNA is one of the most susceptible entities in any kind of free radical induced reactions in living systems. In the present work, the transformation of thymidine (dT) induced by ultrasound (US) was investigated using high resolution mass spectrometry (LC-Q-ToF-MS). dT was subjected to sonolysis under four different frequencies (200, 350, 620 and 1000 kHz) and at three power densities (10.5, 24.5 and 42 W/mL) in aerated as well as argon saturated conditions. A total of twenty modified nucleosides including non-fully characterized dT dimeric compounds were detected by LC-Q-ToF-MS. Out of these products, seven were obtained only in the argon atmosphere and two only in the aerated conditions. Among the identified products, there were base modified products and sugar modified products. The products were formed by the reaction of hydroxyl radical and hydrogen atom. Under aerated conditions, the reactions proceed via the formation of hydroperoxides, while in argon atmosphere disproportionation and radical recombinations predominate. The study provides a complete picture of sonochemical transformation pathways of dT which has relevance in DNA damage under ultrasound exposure.
Chandran, Jisha,Aravind, Usha K.,Aravindakumar
p. 178 - 186
(2015/06/02)

Discovery of a bacterial 5-methylcytosine deaminase
5-Methylcytosine is found in all domains of life, but the bacterial cytosine deaminase from Escherichia coli (CodA) will not accept 5-methylcytosine as a substrate. Since significant amounts of 5-methylcytosine are produced in both prokaryotes and eukaryotes, this compound must eventually be catabolized and the fragments recycled by enzymes that have yet to be identified. We therefore initiated a comprehensive phylogenetic screen for enzymes that may be capable of deaminating 5-methylcytosine to thymine. From a systematic analysis of sequence homologues of CodA from thousands of bacterial species, we identified putative cytosine deaminases where a "discriminating" residue in the active site, corresponding to Asp-314 in CodA from E. coli, was no longer conserved. Representative examples from Klebsiella pneumoniae (locus tag: Kpn00632), Rhodobacter sphaeroides (locus tag: Rsp0341), and Corynebacterium glutamicum (locus tag: NCgl0075) were demonstrated to efficiently deaminate 5-methylcytosine to thymine with values of kcat/Km of 1.4 × 105, 2.9 × 104, and 1.1 × 103 M-1 s-1, respectively. These three enzymes also catalyze the deamination of 5-fluorocytosine to 5-fluorouracil with values of kcat/Km of 1.2 × 105, 6.8 × 104, and 2.0 × 102 M-1 s-1, respectively. The three-dimensional structure of Kpn00632 was determined by X-ray diffraction methods with 5-methylcytosine (PDB id: 4R85), 5-fluorocytosine (PDB id: 4R88), and phosphonocytosine (PDB id: 4R7W) bound in the active site. When thymine auxotrophs of E. coli express these enzymes, they are capable of growth in media lacking thymine when supplemented with 5-methylcytosine. Expression of these enzymes in E. coli is toxic in the presence of 5-fluorocytosine, due to the efficient transformation to 5-fluorouracil.
Hitchcock, Daniel S.,Fedorov, Alexander A.,Fedorov, Elena V.,Almo, Steven C.,Raushel, Frank M.
p. 7426 - 7435
(2015/04/16)

The kinetic mechanism of Human Thymidine Phosphorylase-a molecular target for cancer drug development
Human Thymidine Phosphorylase (HTP), also known as the platelet-derived endothelial cell growth factor (PD-ECGF) or gliostatin, catalyzes the reversible phosphorolysis of thymidine (dThd) to thymine and 2-deoxy-α-d-ribose-1- phosphate (2dR1P). HTP is a key enzyme in the pyrimidine salvage pathway involved in dThd homeostasis in cells. HTP is a target for anticancer drug development as its enzymatic activity promotes angiogenesis. Here, we describe cloning, expression, and purification to homogeneity of recombinant TYMP-encoded HTP. Peptide fingerprinting and the molecular mass value of the homogenous protein confirmed its identity as HTP assessed by mass spectrometry. Size exclusion chromatography showed that HTP is a dimer in solution. Kinetic studies revealed that HTP displayed substrate inhibition for dThd. Initial velocity and isothermal titration calorimetry (ITC) studies suggest that HTP catalysis follows a rapid-equilibrium random bi-bi kinetic mechanism. ITC measurements also showed that dThd and Pi binding are favorable processes. The pH-rate profiles indicated that maximal enzyme activity was achieved at low pH values. Functional groups with apparent pK values of 5.2 and 9.0 are involved in dThd binding and groups with pK values of 6.1 and 7.8 are involved in phosphate binding.
Deves, Candida,Rostirolla, Diana Carolina,Martinelli, Leonardo Kras Borges,Bizarro, Cristiano Valim,Santos, Diogenes Santiago,Basso, Luiz Augusto
p. 592 - 604
(2014/03/21)

Characterization of inosine-uridine nucleoside hydrolase (RihC) from Escherichia coli
A non-specific nucleoside hydrolase from Escherichia coli (RihC) has been cloned, overexpressed, and purified to greater than 95% homogeneity. Size exclusion chromatography and sodium dodecyl sulfate polyacrylamide gel electrophoresis show that the protein exists as a homodimer. The enzyme showed significant activity against the standard ribonucleosides with uridine, xanthosine, and inosine having the greatest activity. The Michaelis constants were relatively constant for uridine, cytidine, inosine, adenosine, xanthosine, and ribothymidine at approximately 480 μM. No activity was exhibited against 2′-OH and 3′-OH deoxynucleosides. Nucleosides in which additional groups have been added to the exocyclic N6 amino group also exhibited no activity. Nucleosides lacking the 5′-OH group or with the 2′-OH group in the arabino configuration exhibited greatly reduced activity. Purine nucleosides and pyrimidine nucleosides in which the N7 or N3 nitrogens respectively were replaced with carbon also had no activity.
Arivett, Brock,Farone, Mary,Masiragani, Ranjith,Burden, Andrew,Judge, Shelby,Osinloye, Adedoyin,Minici, Claudia,Degano, Massimo,Robinson, Matthew,Kline, Paul
p. 656 - 662
(2014/03/21)

Iodine Monochloride Facilitated Deglycosylation, Anomerization, and Isomerization of 3-Substituted Thymidine Analogues
The reaction of thymidine, 3-mono-, and 3,3′,5′-trialkylsubstitued thymidine analogues with iodine monochloride (ICl) was investigated. Treatment with ICl resulted in rapid deglycosylation, anomerization, and isomerization of thymidine and 3-substituted thymidine analogues under various reaction conditions leading to the formation of the nucleobases as the major products accompanied by minor formation of α-furanosidic-, α-pyranosidic-, and β-pyranosidic nucleosides. On the other hand, 3,3′,5′-trisubstitued thymidine analogues were only deglycosylated and anomerized. These results are similar to those observed for the acidic hydrolysis of the glycoside bond in nucleosides, but were presumably caused by the Lewis acid character of an iodine electrophile.
Khalil, Ahmed,Ishita, Keisuke,Ali, Tehane,Tiwari, Rohit,Riachy, Ramy,Toppino, Antonio,Hasabelnaby, Sherifa,Sayfullin, Naum,Oliver, Allen G.,Gallucci, Judith,Huang, Zhenguo,Tjarks, Werner
p. 786 - 799
(2015/10/19)

The photochemistry of thymine in frozen aqueous solution: Trimeric and minor dimeric products
Early work identified three compounds, namely the c,s cyclobutane dimer, the so-called (6-4) photoproduct (5-hydroxy-6-4′-(5-methylpyrimidin- 2′-one)-5,6-dihydrothymine) and a trimer hydrate, as products formed upon UV irradiation of thymine in frozen aqueous solution. More recent work has shown that an (α-4) product, namely α-4′-(5′- methylpyrimidine-2′-one)-thymine, is a likely product formed under these reaction conditions. During a thorough reinvestigation of the photochemistry of Thy in ice at -78.5°C, we found that a variety of other products could be detected. In addition to the c,s dimer, the other three known cyclobutane dimers, namely the c,a, t,s and t,a forms, are produced, although in considerably smaller amounts. The so-called spore product of thymine (5,6-dihydro-5-(α-thyminyl)thymine) is likewise formed. Two other dimers have been identified as minor products; one of these has been determined to be 5-(thymin-3-yl)-5,6-dihydrothymine and the other has been tentatively assigned to be a (5-4) adduct (6-hydroxy-5-4′-(5-methylpyrimidin-2′-one)-5,6- dihydrothymine). Compounds with the behavior expected of true trimeric compounds have been isolated via HPLC and characterized by mass spectrometry and photochemical behavior. One of these materials, putatively containing an oxetane ring, decomposes thermally to a secondary trimeric product that is then converted into the known trimer hydrate.
Shetlar, Martin D.,Basus, Vladimir J.
p. 631 - 639
(2013/06/26)

The muraminomicin biosynthetic gene cluster and enzymatic formation of the 2-deoxyaminoribosyl appendage
Muraminomicin is a lipopeptidyl nucleoside antibiotic produced by Streptosporangium amethystogenes SANK 60709. Similar to several members of this antibiotic family such as A-90289 and muraymycin, the structure of muraminomicin consists of a disaccharide comprised of two modified ribofuranose units linked by an O-β(1 → 5) glycosidic bond; however, muraminomicin holds the distinction in that both ribose units are 2-deoxy sugars. The biosynthetic gene cluster of muraminomicin has been identified, cloned and sequenced, and bioinformatic analysis revealed a minimum of 24 open reading frames putatively involved in the biosynthesis, resistance, and regulation of muraminomicin. Fives enzymes are likely involved in the assembly and attachment of the 2,5-dideoxy-5-aminoribose saccharide unit, and two are now functionally assigned and characterized: Mra20, a 5′-amino-2′,5′-dideoxyuridine phosphorylase and Mra23, a UTP:5-amino-2,5-dideoxy-α-d-ribose-1-phosphate uridylyltransferase. The cumulative results are consistent with the incorporation of the ribosyl appendage of muraminomicin via the archetypical sugar biosynthetic pathway that parallels A-90289 biosynthesis, and the specificity for this appendage is dictated primarily by the two characterized enzymes. The Royal Society of Chemistry 2013.
Chi, Xiuling,Baba, Satoshi,Tibrewal, Nidhi,Funabashi, Masanori,Nonaka, Koichi,Van Lanen, Steven G.
p. 239 - 243
(2013/03/13)

A comparison between immobilized pyrimidine nucleoside phosphorylase from Bacillus subtilis and thymidine phosphorylase from Escherichia coli in the synthesis of 5-substituted pyrimidine 2′-deoxyribonucleosides
Pyrimidine nucleoside phosphorylase from Bacillus subtilis (BsPyNP, E.C. 2.4.2.3) and thymidine phosphorylase from Escherichia coli (EcTP, E.C. 2.4.2.4) were used, as immobilized enzymes, in the synthesis of 5-halogenated pyrimidine 2′-deoxyribonucleosides (14-18) by transglycosylation in fully aqueous medium. From the comparative study of the two biocatalysts, no remarkable differences emerged about their substrate specificity, bioconversion yield, stability in organic cosolvents (DMF and MeCN). Moreover, both biocatalysts could be recycled for at least 5 times with no loss of the productivity. Both enzymes do not accept arabinonucleosides and 2′,3′- dideoxynucleosides as substrates, whereas they catalyze bioconversions involving 5′-deoxyribonucleosides and 5-halogenated uracils. The synthesis of compounds 14-18 proceeded at a similar conversion (33-68% for BsPyNP and 25-62% for EcTP, respectively). Immobilization was found to exert, for both the biocatalysts, a dramatic enhancement of stability upon incubation in MeCN. Optimization of 5-fluoro-2′-deoxyuridine (14) synthesis (pH 7.5, 10 mM phosphate buffer, nucleoside/nucleobase 3:1 molar ratio) and subsequent scale-up afforded the target compound in 73% (EcTP) or 76% (BsPyNP) conversion (about 9 g/L).
Serra, Immacolata,Bavaro, Teodora,Cecchini, Davide A.,Daly, Simona,Albertini, Alessandra M.,Terreni, Marco,Ubiali, Daniela
p. 16 - 22
(2013/10/22)

Enzymatic synthesis of 2-deoxy-β-d-ribonucleosides of 8-azapurines and 8-aza-7-deazapurines
The enzymatic synthesis of 8-azapurine and 8-aza-7-deazapurine 2-deoxyribonucleosides has been studied. Two methods have been used: (i) transglycosylation employing 2-deoxyguanosine, 2-deoxycytidine, 2-deoxyuridine, and 2-deoxythymidine as 2-deoxy-d-ribofuranose donors and recombinant E. coli purine nucleoside phosphorylase (PNP) as biocatalyst, and (ii) one-pot synthesis from 2-deoxy-d-ribose and nucleobases employing recombinant E. coli ribokinase (RK), phosphopentomutase (PPM) and PNP as biocatalysts. Good substrate activity was observed for all bases studied except 2-amino-8-aza-6-chloro-7-deazapurine, which afforded the desired N9-nucleoside in moderate yield due to very low solubility of the base and partial replacement of C6-chloro atom of the base and formed nucleoside with a hydroxy group. The participation of Ser90 Oγ of E. coli PNP in the binding of 8-aza-7-deazapurines in the catalytic center of PNP followed by the formation of a productive complex and glycosidic bond is suggested. Georg Thieme Verlag Stuttgart · New York.
Stepchenko, Vladimir A.,Seela, Frank,Esipov, Roman S.,Miroshnikov, Anatoly I.,Sokolov, Yuri A.,Mikhailopulo, Igor A.
experimental part
p. 1541 - 1545
(2012/09/08)

Characterization of pyrimidine nucleoside phosphorylase of Mycoplasma hyorhinis: Implications for the clinical efficacy of nucleoside analogues
In the present paper we demonstrate that the cytostatic and antiviral activity of pyrimidine nucleoside analogues is markedly decreased by a Mycoplasma hyorhinis infection and show that the phosphorolytic activity of the mycoplasmas is responsible for this. Since mycoplasmas are (i) an important cause of secondary infections in immunocompromised (e.g. HIV infected) patients and (ii) known to preferentially colonize tumour tissue in cancer patients, catabolic mycoplasma enzymesmay compromise efficient chemotherapy of virus infections and cancer. In the genome of M. hyorhinis, a TP (thymidine phosphorylase) gene has been annotated. This gene was cloned, expressed in Escherichia coli and kinetically characterized. Whereas the mycoplasma TP efficiently catalyses the phosphorolysis of thymidine (Km = 473 μM) and deoxyuridine (Km = 578 μM), it prefers uridine (K m =92 μM) as a substrate. Our kinetic data and sequence analysis revealed that the annotated M. hyorhinis TP belongs to the NP (nucleoside phosphorylase)-II class PyNPs (pyrimidine NPs), and is distinct from the NP-II class TP and NPI class UPs (uridine phosphorylases). M. hyorhinis PyNP also markedly differs from TP and UP in its substrate specificity towards therapeutic nucleoside analogues and susceptibility to clinically relevant drugs. Several kinetic properties of mycoplasma PyNP were explained by in silico analyses. The Authors Journal compilation
Vande Voorde, Johan,Gago, Federico,Vrancken, Kristof,Liekens, Sandra,Balzarini, Jan
experimental part
p. 113 - 123
(2012/10/23)

PHOSPHORAMIDATE DERIVATIVES OF 5 - FLUORO - 2 ' - DEOXYURIDINE FOR USE IN THE TREATMENT OF CANCER
Phosphoramidate derivatives of 5-fluoro-2'-deoxyuridine are disclosed for use in the treatment of cancer, especially in the treatment of cancer where the patient shows resistance, for example, in a patient with cells with a lowered level of nucleoside transporter proteins and/or with nucleoside kinase-deficient cells and/or with mycoplasma-infected cells and/or with cells with a raised level of thymidylate synthase.
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Page/Page column 66-67

(2012/09/21)

Investigation of reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides
Model 3′-azido-3′-deoxynucleosides with thiol or vicinal dithiol substituents at C2′ or C5′ were synthesized to study reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides. Esterification of 5′-(tert-
Dang, Thao P.,Sobczak, Adam J.,Mebel, Alexander M.,Chatgilialoglu, Chryssostomos,Wnuk, Stanislaw F.
experimental part
p. 5655 - 5667
(2012/09/25)

Photorepair of cyclobutane pyrimidine dimers by 8-oxopurine nucleosides
The 8-oxopurine nucleosides 2′,3′,5′-tri-O-acetyl-8-oxo- 7,8-dihydroguanosine (OG) and 2′,3′,5′-tri-O-acetyl- ribosyluric acid (RU) were studied for their ability to mediate the photochemical (λ>300nm) reversion of cyclobutane pyrimidine dimers to their parent pyrimidines thymine and uracil. The bimolecular reactions of these monomers proceeded at very slow rates compared with recently published work using oligonucleotide contexts; nevertheless, it was possible to make comparisons between the efficacy of OG and RU as photocatalysts as a function of pH. Although RU has a lower redox potential and anionic character, it was only equivalent to OG in facilitating thymine dimer photorepair over a broad pH range. Only OG showed pH-dependent behavior with higher activity at pH 8-9 where the base becomes deprotonated. Despite the overall low activity of OG and RU, the results are instructive with respect to a comparison of the two 8-oxopurines, and support the hypothesis that 8-oxopurine nucleosides may have played primordial roles as precursors to modern-day flavins in redox reactions of the RNA world. Copyright
Nguyen, Khiem Van,Burrows, Cynthia J.
experimental part
p. 574 - 577
(2012/08/28)

Biosynthetic origin and mechanism of formation of the aminoribosyl moiety of peptidyl nucleoside antibiotics
Several peptidyl nucleoside antibiotics that inhibit bacterial translocase I involved in peptidoglycan cell wall biosynthesis contain an aminoribosyl moiety, an unusual sugar appendage in natural products. We present here the delineation of the biosynthetic pathway for this moiety upon in vitro characterization of four enzymes (LipM-P) that are functionally assigned as (i) LipO, an l-methionine:uridine-5′-aldehyde aminotransferase; (ii) LipP, a 5′-amino-5′-deoxyuridine phosphorylase; (iii) LipM, a UTP:5-amino-5-deoxy-α-d-ribose-1-phosphate uridylyltransferase; and (iv) LipN, a 5-amino-5-deoxyribosyltransferase. The cumulative results reveal a unique ribosylation pathway that is highlighted by, among other features, uridine-5′-monophosphate as the source of the sugar, a phosphorylase strategy to generate a sugar-1-phosphate, and a primary amine-requiring nucleotidylyltransferase that generates the NDP-sugar donor.
Chi, Xiuling,Pahari, Pallab,Nonaka, Koichi,Van Lanen, Steven G.
supporting information; experimental part
p. 14452 - 14459
(2011/11/04)

The cytostatic activity of NUC-3073, a phosphoramidate prodrug of 5-fluoro-2′-deoxyuridine, is independent of activation by thymidine kinase and insensitive to degradation by phosphorolytic enzymes
A novel phosphoramidate nucleotide prodrug of the anticancer nucleoside analogue 5-fluoro-2′-deoxyuridine (5-FdUrd) was synthesized and evaluated for its cytostatic activity. Whereas 5-FdUrd substantially lost its cytostatic potential in thymidine kinase (TK)-deficient murine leukaemia L1210 and human lymphocyte CEM cell cultures, NUC-3073 markedly kept its antiproliferative activity in TK-deficient tumour cells, and thus is largely independent of intracellular TK activity to exert its cytostatic action. NUC-3073 was found to inhibit thymidylate synthase (TS) in the TK-deficient and wild-type cell lines at drug concentrations that correlated well with its cytostatic activity in these cells. NUC-3073 does not seem to be susceptible to inactivation by catabolic enzymes such as thymidine phosphorylase (TP) and uridine phosphorylase (UP). These findings are in line with our observations that 5-FdUrd, but not NUC-3073, substantially loses its cytostatic potential in the presence of TP-expressing mycoplasmas in the tumour cell cultures. Therefore, we propose NUC-3073 as a novel 5-FdUrd phosphoramidate prodrug that (i) may circumvent potential resistance mechanisms of tumour cells (e.g. decreased TK activity) and (ii) is not degraded by catabolic enzymes such as TP which is often upregulated in tumour cells or expressed in mycoplasma-infected tumour tissue.
Vande Voorde, Johan,Liekens, Sandra,McGuigan, Christopher,Murziani, Paola G.S.,Slusarczyk, Magdalena,Balzarini, Jan
experimental part
p. 441 - 452
(2012/01/14)

Opened-ring adducts of 5-methylcytosine and 1,5-dimethylcytosine with amines and water and evidence for an opened-ring hydrate of 2′- deoxycytidine
A variety of nucleic acid components and related compounds undergo photoreaction with water to form so-called photohydrates (e.g. uracil forms 6-hydroxy-5,6-dihydrouracil). However, the corresponding hydrates of 5-methylcytosine (a minor nucleobase in eukaryotic DNA) and related compounds have not been characterized. We report the preparation of opened-ring forms of such products for 5-methylcytosine (m5C) and 1,5-dimethylcytosine (DMC). This was accomplished via thermal reaction of ring-opened amine adducts (e.g. N-carbamoyl-3-amino-2-methylacrylamidine (IVa) or N-(N′-methylcarbamoyl)- 3-amino-2-methylacrylamidine (IVb)) produced by photo-induced reactions of m5C with ammonia or methylamine. When these adducts were treated with dilute trifluoroacetic acid, the amino group at the 3-position was replaced with a hydroxyl group; with IVa, N-carbamoyl-3-hydroxy-2-methylacrylamidine (Va) was formed, while reaction of IVb led to N-(N′-methylcarbamoyl)-3-hydroxy-2- methylacrylamidine (Vb). These compounds are ring-opened isomers of 5,6-dihydro-6-hydroxy-5-methylcytosine (Ia and IIa) and 5,6-dihydro-6-hydroxy-1, 5-dimethylcytosine (Ib and IIb). Compounds Va and Vb each undergo thermal ring closure reactions to form two unstable compounds with chemical and UV spectral properties expected for Ia and IIa (or Ib and IIb). The latter compounds have been identified as minor products in UV-irradiated aqueous solutions of m5C and DMC. Evidence is also presented that the 2′-deoxycytidine photohydrates coexist with an opened-ring form, possibly similar in nature to Vb. The nucleobase 5-methylcytosine (m5C) reacts photochemically with ammonia to form an opened-ring adduct (IVa); similar reactions occur with 1,5-dimethylcytosine and with methylamine. Subjection of such adducts to hydrolysis in dilute acid (e.g. 0.1% trifluoracetic acid) produces opened-ring hydrates of m5C (Va) and DMC. Photoreaction of the nucleoside 2′-deoxycytidine in water results in formation of closed-ring hydrates that equilibrate thermally with a compound that has the UV spectral properties expected for an adduct similar in nature to Va.
Shetlar, Martin D.,Chung, Janet
experimental part
p. 818 - 832
(2012/07/27)

Serendipitous discovery of a zidovudine guanidine complex: A superior process for the production of zidovudine
A superior process for the commercial production of zidovudine (AZT) has been developed. It was discovered that an AZT-guanidine complex formed when a crude zidovudine solution was treated with guanidine. This readily precipitated from protic solvents resulting in the exclusion of impurities and permitted the development of a superior isolation and purification of AZT.
Radatus, Bruno K.
experimental part
p. 1281 - 1286
(2012/01/13)

Synthesis of 3-fluoro-6-S-(2-S-pyridyl) nucleosides as potential lead cytostatic agents
The 3-deoxy-3-fluoro-6-S-(2-S-pyridyl)-6-thio-β-d-glucopyranosyl nucleoside analogs 7 were prepared via two facile synthetic routes. Their precursors, 3-fluoro-6-thio-glucopyranosyl nucleosides 5a-e, were obtained by the sequence of deacetylation of 3-deoxy-3-fluoro-β-d-glucopyranosyl nucleosides 2a-e, selective tosylation of the primary OH of 3 and finally treatment with potassium thioacetate. The desired thiolpyridine protected analogs 7a-c,f,g were obtained by the sequence of deacetylation of 5a-c followed by thiopyridinylation and/or condensation of the corresponding heterocyclic bases with the newly synthesized peracetylated 6-S-(2-S-pyridyl) sugar precursor 13, which was obtained via a novel synthetic route from glycosyl donor 12. None of the compounds 6 and 7 showed antiviral activity, but the 5-fluorouracil derivative 7c and particularly the uracil derivative 7b were endowed with an interesting and selective cytostatic action against a variety of murine and human tumor cell cultures.
Tsoukala, Evangelia,Tzioumaki, Niki,Manta, Stella,Riga, Alexandra,Balzarini, Jan,Komiotis, Dimitri
experimental part
p. 285 - 293
(2011/02/23)

Michael versus retro-Michael reaction in the regioselective synthesis of N-1 and N-3 uracil adducts
By controlling the temperature or reaction time in the base-catalysed Michael-type addition of 5-substituted uracil derivatives we were able to synthesise N-1 or N-3 uracil adducts using methyl acrylate and acrylonitrile as acceptors. The mechanism of this chemical inequivalence was established using 1H NMR spectroscopic studies. The investigations revealed that formation of the N-1 adduct was achievable under kinetically controlled conditions irrespective to the type of the base used (TEA, DBU). In turn, synthesis of the N-3 adducts proceeded from the initially formed N-1,N-3 diadduct via a retro-Michael reaction which dominates at elevated temperature or prolonged reaction time.
Boncel, S?awomir,McZka, MacIej,Walczak, Krzysztof Z.
scheme or table
p. 8450 - 8457
(2010/12/25)

PROCESS FOR STRAIGHTENING KERATIN FIBRES WITH A HEATING MEANS AND DENATURING AGENTS
The invention relates to a process for straightening keratin fibres, comprising: (i) a step in which a straightening composition containing at least two denaturing agents is applied to the keratin fibres, (ii) a step in which the temperature of the keratin fibres is raised, using a heating means, to a temperature of between 110 and 250° C.
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(2010/03/02)

HUMANIZED ANTI-EGFL7 ANTIBODIES AND METHODS USING SAME
The present invention concerns antibodies to EGFL7 and the uses of same.
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(2010/12/29)

Studies on the synthesis of N′-acetyl AZA-analogues of Ganciclovir - Unexpected liability of N′-(2-hydroxyethyl)-azanucleosides under basic conditions
The O′-pivaloyl diesters of N′-acetyl-azanucleosides were obtained from N-[1,3-di(pivaloyloxy)prop-2-yl]-N-(pivaloyloxymethyl)acetamide and a silylated nucleobase under Vorbruggen′s conditions. Unexpectedly, de-pivaloylation of the diesters under basic conditions afforded the corresponding nucleobase and N-acetylserinol. Mechanistic investigations showed that these products result from the following cascade of spontaneous transformations initiated by the mono de-pivaloylation of the starting diesters. N′-Deacetylation of the resultant mono-esters via the intramolecular N-O acetyl migration is the key step of the cascade; the corresponding NH-azanucleosides in the form of O-acetyl-O′-pivaloyl diesters are formed. Fragmentation of these diester intermediates gives the nucleobase and O-acetyl-O'-pivaloylserinol. Conversion of the latter to N-acetylserinol involves the selective O-N acetyl migration followed by de-pivaloylation of the resulting N-acetyl-O-pivaloylserinol. Copyright Taylor and Francis Group, LLC.
Koszytkowska-Stawinska, Mariola
experimental part
p. 768 - 785
(2011/05/04)

Disposition of [1′-14C]stavudine after oral administration to humans
The disposition of stavudine, a potent and orally active nucleoside reverse transcriptase inhibitor, was investigated in six healthy human subjects. Before dosing humans with [1′-14C]stavudine, a tissue distribution study was performed in Long-Evans rats. Results from this study showed no accumulation of radioactivity in any of the tissues studied, indicating that the position of the 14Clabel on the molecule was appropriate for the human study. After a single 80-mg (100 μCi) oral dose of [1′- 14C]stavudine, approximately 95% of the radioactive dose was excreted in urine with an elimination half-life of 2.35 h. Fecal excretion was limited, accounting for only 3% of the dose. Unchanged stavudine was the major drug-related component in plasma (61% of area under the plasma concentration-time curve from time zero extrapolated to infinite time of the total plasma radioactivity) and urine (67% of dose). The remaining radioactivity was associated with minor metabolites, including mono- and bis-oxidized stavudine, glucuronide conjugates of stavudine and its oxidized metabolite, and an N-acetylcysteine (NAC) conjugate of the ribose (M4) after glycosidic cleavage. Formation of metabolite M4 was shown in human liver microsomes incubated with 2′,3′-didehydrodideoxyribose, the sugar base of stavudine, in the presence of NAC. In addition, after similar microsomal incubations fortified with GSH, two GSH conjugates, 3′-GS-deoxyribose and 1′-keto-2′,3′-dideoxy-3′-GS-ribose, were observed. This suggests that 2′,3′-didehydrodideoxyribose underwent cytochrome P450-mediated oxidation leading to an epoxide intermediate, 2′,3′- ribose epoxide, followed by GSH addition. In conclusion, absorption and elimination of stavudine were rapid and complete after oral dosing, with urinary excretion of unchanged drug as the predominant route of elimination in humans. Copyright
Zhou, Lian,Kaul, Sanjeev,Liu-Kreyche, Peggy,Tran, Scott B.,Espina, Robert R.,Warrack, Bethanne M.,Roongta, Vikram A.,Iyer, Ramaswamy A.
experimental part
p. 655 - 666
(2011/02/26)

Transition state analysis of thymidine hydrolysis by human thymidine phosphorylase
Human thymidine phosphorylase (hTP) is responsible for thymidine (dT) homeostasis, and its action promotes angiogenesis. In the absence of phosphate, hTP catalyzes a slow hydrolytic depyrimidination of dT yielding thymine and 2-deoxyribose (dRib). Its transition state was characterized using multiple kinetic isotope effect (KIE) measurements. Isotopically enriched thymidines were synthesized enzymatically from glucose or (deoxy)ribose, and intrinsic KIEs were used to interpret the transition state structure. KIEs from [1′- 14C]-, [1-15N]-, [1′-3H]-, [2′R-3H]-, [2′S-3H]-, [4′- 3H]-, and [5′-3H]dTs provided values of 1.033 ± 0.002, 1.004 ± 0.002, 1.325 ± 0.003, 1.101 ± 0.004, 1.087 ± 0.005, 1.040 ± 0.003, and 1.033 ± 0.003, respectively. Transition state analysis revealed a stepwise mechanism with a 2-deoxyribocation formed early and a higher energetic barrier for nucleophilic attack of a water molecule on the high energy intermediate. An equilibrium exists between the deoxyribocation and reactants prior to the irreversible nucleophilic attack by water. The results establish activation of the thymine leaving group without requirement for phosphate. A transition state constrained to match the intrinsic KIEs was found using density functional theory. An active site histidine (His116) is implicated as the catalytic base for activation of the water nucleophile at the rate-limiting transition state. The distance between the water nucleophile and the anomeric carbon (rC-O) is predicted to be 2.3 A at the transition state. The transition state model predicts that deoxyribose adopts a mild 3′-endo conformation during nucleophilic capture. These results differ from the concerted bimolecular mechanism reported for the arsenolytic reaction (Birck, M. R.; Schramm, V. L. J. Am. Chem. Soc. 2004, 126, 2447-2453).
Schwartz, Phillip A.,Vetticatt, Mathew J.,Schramm, Vern L.
supporting information; experimental part
p. 13425 - 13433
(2010/12/19)

Self-sacrificing acetylation observed during attempted desilylation of 1-[4-benzenesulfonyl-3-O-(tert-butyldimethylsilyl)-2-deoxy-5-O-methanesulfonyl- α-l-threo-pentofuranosyl]thymine
Desilylation of 1-[4-benzenesulfonyl-3-O-(tert-butyldimethylsilyl)-2-deoxy- 5-O-methanesulfonyl-α-l-threo-pentofuranosyl]thymine (4) with Bu 4NF/THF, when carried out at room temperature, gave four products. Among these, there were 1-[3-O-acetyl-4-benzenesulfonyl-2-deoxy-5-O- methanesulfonyl-α-l-threo-pentofuranosyl]thymine (7) and thymine. A possible reaction mechanism is proposed, which suggests the origin of 3′-O-acetyl group of 7 and thymine as well as structures of the other two products (9a and 9b).
Shimada, Hisashi,Kubota, Yutaka,Tanaka, Hiromichi
body text
p. 4253 - 4255
(2010/09/07)

New [11C]phosgene based synthesis of [11C]pyrimidines for positron emission tomography
Thymine, 5-FU, and uracil were successfully synthesized through a procedure involving a cyclocondensation of triphosgene with newly developed (α-substituted β-aminoacrylamides intermediates (1a, X= Me; 1b, X= F; 1c, X= H). The radioligands [2-11C]thymine and [2- 11C]5-fluorouracil were synthesized in high radiochemical yields in 16-17 minutes from the end of bombardment by applying the cyclocondensation method with [11C]COCl2.
Seki, Koh-Ichi,Nishijima, Ken-Ichi,Sanoki, Kimihito,Kuge, Yuji,Takahashi, Masayuki,Akizawa, Hiromichi,Tamaki, Nagara,Wiebe, Leonard I.,Ohkura, Kazue
experimental part
p. 1307 - 1321
(2010/10/03)

Novel acyclic amide-conjugated nucleosides and their analogues
An effective one-step synthesis of new amide-conjugated nucleosides and their analogues, in the presence of 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4- methylmorpholinium chloride (DMT-MM) as the condensing agent, is presented. Substrate subunits carrying carboxylic group were obtained by acidic hydrolysis of Michael-type adducts of various 5-substituted uracil derivatives to methyl acrylate. Amine substrate was synthesized by reduction of 1-(2′- cyanoethyl)thymine with sodium borohydride in the presence of nickel (II) chloride as catalyst. Other applied amine substrates were 5′-amino- 5′-deoxythymidine and 5-aminouracil. Copyright Taylor & Francis Group, LLC.
Boncel, Slawomir,Walczak, Krzysztof
experimental part
p. 103 - 117
(2009/06/18)

ANTIBODIES TO INSULIN-LIKE GROWTH FACTOR RECEPTOR
The invention provides various antibodies that bind to insulin-like growth factor-I receptor (IGF-1R), methods for making such antibodies, compositions and articles incorporating such antibodies, and their uses in treating, for example, cancer or aging. The antibodies include murine, chimeric, and humanized antibodies.
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(2009/04/24)

ANTIBODIES TO LYMPHOTOXIN-ALPHA
The invention provides various antibodies that bind to lymphotoxin-α, methods for making such antibodies, compositions and articles incorporating such antibodies, and their uses in treating, for example, an autoimmune disorder. The antibodies include murine, chimeric, and humanized antibodies.
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(2009/12/05)

Antibodies and immunoconjugates and uses therefor
Anti-STEAP-1 antibodies and immunoconjugates thereof are provided. Methods of using anti-STEAP-1 antibodies and immunoconjugates thereof are provided.
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(2009/12/04)

Fluorinase-coupled base swaps: Synthesis of [18F]-5′- deoxy-5′-fluorouridines
(Chemical Equation Presented) Making F-ases: One-pot fluorination/base-swap biotransformations were developed by coupling the fluorinase enzyme to nucleoside phosphorylases to generate 5′-deoxy-5′-fluoronucleosides (FDAs). These biotransformations are amenable to radiolabeling syntheses starting from [18F]fluoride ion, as exemplified by the synthesis of [18F]-5′-deoxy-5′-fluorouridines (see scheme), and demonstrate a new application of fluorinase as a catalyst for 18F-C bond formation.
Winkler, Margit,Domarkas, Juozas,Schweiger, Lutz F.,O'Hagan, David
supporting information; experimental part
p. 10141 - 10143
(2009/05/30)

Protecting groups transfer: Unusual method of removal of tr and TBDMS groups by transetherification
The triphenylmethyl (Tr) group undergoes a transfer (transetherification or disproportionation) between the molecules of 5'-O-Tr-2'-deoxynucleosides in a process mediated by anhydrous sulfates of Cu+2, Fe+2, or Ni+2 to yield mixtures of 3',5'-bis-O-Tr and 3'-O-Tr products. If phenylmethanol is present in a reaction medium, detritylation results with concomitant formation of phenylmethyl triphenylmethyl ether. The behavior of t-butyldimethylsilyl (TBDMS) group in 5'-O-TBDMS-2'-deoxynucleosides is exactly the same. Such type of transetherifications was not observed before for the O-Tr and O-TBDMS groups. Copyright Taylor & Francis Group, LLC.
Cabral, Nadia L. D.,Thiessen, Luciano Hoeltgebaum,Doboszewski, Bogdan
p. 931 - 948
(2008/12/21)

Photochemical generation of oligodeoxynucleotide containing a C4′-oxidized abasie site and its efficient amine modification: Dependence on structure and microenvironment
(Chemical Equation Presented) Bleomycin-induced oxidative DNA damage under limited oxygen conditions results in the formation of the C4′-oxidized abasic site (1). We synthesized the oligodeoxynucleotides (ODN) 5, which contains 4′-o-nitrobenzyloxythymidine (3), and 6, which contains 2-nitrobenzyloxy-4′-methoxy-2′-deoxy-D-ribofuranoside (4) as the caged precursors of 7, an ODN containing 1, to study its reactivity with amines Photoirradiation of the single- and double-stranded 5 led to the formation of 7. Uncaging of the duplex was faster and the yield of 7 was higher with the double-stranded than with the single-stranded ODN. It was suggested that a low dielectric environment of the o-nitrobenzyloxy group in the minor groove of the duplex might accelerate the uncaging rate. Similarly, 6 and its duplex yielded 7 by photoirradiation However, the yields of 7 were lower than those of 5, and duplex formation slowed the uncaging rate. Reaction of the obtained 7 with an amine resulted in the formation of the lactam 2b in good yield in both single- and double-stranded forms, showing that amine modification of biomolecules by an ODN containing 1 is possible under physiologic conditions.
Usui, Kazuteru,Aso, Mariko,Fukuda, Mitsuhiro,Suemune, Hiroshi
p. 241 - 248
(2008/09/19)

α,β-Methylene-2′-deoxynucleoside 5′-triphosphates as noncleavable substrates for DNA polymerases: Isolation, characterization, and stability studies of novel 2′-deoxycyclonucleosides, 3,5′-cyclo-dG, and 2,5′-cyclo-dT
We report synthesis and characterization of a complete set of α,β-methylene-2′-dNTPs (α,β-m-dNTP; N = A, C, T, G, 12-15) in which the α,β-oxygen linkage of natural dNTP was replaced by a methylene group. These nucleotides were designed to be noncleavable substrates for DNA polymerases. Synthesis entails preparation of 2′-deoxynucleoside 5′-diphosphate precursors, followed by an enzymatic γ-phosphorylation. All four synthesized α,β-m-dNTPs were found to be potent inhibitors of polymerase β, with Ki values ranging 1-5 μM. During preparation of the dG and dT derivatives of α,β-methylene diphosphate, we also isolated significant amounts of 3,5′-cyclo-dG (16) and 2,5′-cyclo-dT (17), respectively. These novel 2′-deoxycyclonucleosides were formed via a base-catalyzed intramolecular cyclization (N3 → C5′ and O2 → C5′, respectively). In acidic solution, both 16 and 17 underwent glycolysis, followed by complete depurination. When exposed to alkaline conditions, 16 underwent an oxidative deamination to produce 3,5′-cyclo-2′-deoxyxanthosine (19), whereas 17 was hydrolyzed exclusively to dT.
Liang, Fengting,Jain, Nidhi,Hutchens, Troy,Shock, David D.,Beard, William A.,Wilson, Samuel H.,Chiarelli, M. Paul,Cho, Bongsup P.
experimental part
p. 6460 - 6470
(2009/10/23)

Substrate specificity of thymidine phosphorylase of E. coli: Role of hydroxyl groups
Substrate specificity of E. coli thymidine phosphorylase to pyrimidine nucleoside modified at 5′-, 3′-, and 2′-positions of sugar moiety has been studied. Equilibrium (Keq) and kinetics constants of phosphorolysis reaction of nucleosides were measured. Th
Panova, Natalya G.,Alexeev, Cyril S.,Polyakov, Konstantin M.,Gavryushov, Sergei A.,Kritzyn, Anatoliy M.,Mikhailov, Sergey N.
scheme or table
p. 1211 - 1214
(2009/04/06)

Kinetic parameters and recognition of thymidine analogues with varying functional groups by thymidine phosphorylase
Thymidine phosphorylase (TP, EC 2.4.2.4) recognized the structure of the substrate with high specificity, via both the base and the ribosyl moieties. The replacement of 3′-OH of thymidine markedly influenced its catalytic activity with TP. The conversion
Hatano, Akihiko,Harano, Aiko,Takigawa, Yoshikatsu,Naramoto, Yasuhiro,Toda, Keisuke,Nakagomi, Yuuichi,Yamada, Hideyuki
p. 3866 - 3870
(2008/12/20)

Electrophile-promoted addition of hydroxymethylphosphonate to 4′,5′-didehydronucleosides: a way to novel isosteric analogues of 5′-nucleotides
An electrophile-promoted addition of dialkyl-hydroxymethylphosphonate to the protected 4′,5′-didehydronucleosides resulted in an epimeric mixture of 4′-dialkylphosphonomethoxy derivatives of 2′,5′-dideoxynucleosides, novel analogues of 2′-deoxynucleoside 5′-monophosphates. Several types of electrophiles (pyridinium tosylate, NIS, NBS, MCPBA and others) were evaluated in addition reactions with 4′,5′-didehydrothymidine. Out of them, pyridinium tosylate was found to have a practical usefulness in these transformations. Its use has led to the preparation of a series of 4′-phosphonomethoxy derivatives of common 2′-deoxynucleosides. On biological screening, these free phosphonic acids exerted no significant cytostatic or antiviral activity.
To?ík, Zdeněk,Dvo?áková, Ivana,Liboska, Radek,Budě?ínsky, Milo?,Masojídková, Milena,Rosenberg, Ivan
p. 4516 - 4534
(2008/02/01)